Dodders (Cuscutaspp.) are obligate parasitic plants that obtain water and nutrients from the stems of host plants via specialized feeding structures called haustoria. Dodder haustoria facilitate bidirectional movement of viruses, proteins and mRNAs between host and parasite1, but the functional effects of these movements are not known. Here we show thatCuscuta campestrishaustoria accumulate high levels of many novel microRNAs (miRNAs) while parasitizingArabidopsis thaliana. Many of these miRNAs are 22 nucleotides in length. Plant miRNAs of this length are uncommon, and are associated with amplification of target silencing through secondary short interfering RNA (siRNA) production2. SeveralA. thalianamRNAs are targeted by 22-nucleotideC. campestrismiRNAs during parasitism, resulting in mRNA cleavage, secondary siRNA production, and decreased mRNA accumulation. Hosts with mutations in two of the loci that encode target mRNAs supported significantly higher growth ofC. campestris. The same miRNAs that are expressed and active whenC. campestrisparasitizesA. thalianaare also expressed and active when it infectsNicotiana benthamiana. Homologues of target mRNAs from many other plant species also contain the predicted target sites for the inducedC. campestrismiRNAs. These data show thatC. campestrismiRNAs act as trans-species regulators of host-gene expression, and suggest that they may act as virulence factors during parasitism.